Soroor Hediyeh zadeh
| Snapshot Date: 2024-10-27 02:55 -0400 (Sun, 27 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/oppar |
| git_branch: devel |
| git_last_commit: 0170bdd |
| git_last_commit_date: 2024-04-30 10:50:23 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-28 11:49 -0400 (Mon, 28 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4501 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4761 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4504 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4535 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4491 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1469/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oppar 1.33.0 (landing page) Soroor Hediyeh zadeh
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the oppar package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oppar.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: oppar |
| Version: 1.33.0 |
| Command: rm -rf oppar.buildbin-libdir && mkdir oppar.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oppar_1.33.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oppar.buildbin-libdir |
| StartedAt: 2024-10-28 05:54:27 -0400 (Mon, 28 Oct 2024) |
| EndedAt: 2024-10-28 05:54:44 -0400 (Mon, 28 Oct 2024) |
| EllapsedTime: 16.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: oppar_1.33.0.tgz |
| PackageFileSize: 5.321 MiB |
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### Running command:
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### rm -rf oppar.buildbin-libdir && mkdir oppar.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oppar_1.33.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oppar.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oppar.buildbin-libdir oppar_1.33.0.tar.gz'
>>>>>>>
* installing *source* package ‘oppar’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_oppar.c -o R_init_oppar.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kernel_estimation.c -o kernel_estimation.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ks_test.c -o ks_test.o
ks_test.c:22:9: warning: unused variable 'mx_value' [-Wunused-variable]
double mx_value = 0.0;
^
1 warning generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o oppar.so R_init_oppar.o kernel_estimation.o ks_test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/oppar.buildbin-libdir/00LOCK-oppar/00new/oppar/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘gsva’ in package ‘oppar’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: multiple methods tables found for ‘gsva’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘gsva’
** testing if installed package keeps a record of temporary installation path
* DONE (oppar)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR oppar.buildbin-libdir/oppar/libs/oppar.so
>>>>>>>
>>>>>>> Paths before fix:
oppar.buildbin-libdir/oppar/libs/oppar.so:
oppar.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "oppar.buildbin-libdir/oppar/libs/oppar.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "oppar.buildbin-libdir/oppar/libs/oppar.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "oppar.buildbin-libdir/oppar/libs/oppar.so"
>>>>>>> Paths after fix:
oppar.buildbin-libdir/oppar/libs/oppar.so:
oppar.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)